Submission Results

Sequence Name: Not Available

GenBank Accession Number: 1027763300

GenInfo (GI) Number: 0000000000

Download Results: 1027763300.PHASTER.zip

gi|00000000|ref|NZ_LXOM01000216.1| Salmonella enterica strain CU013109 PROKKA_contig000218, whole 12226, gc%: 48.74%

Download summary as .txt file: summary.txt file_download

Total: 1 prophage regions have been identified, of which 0 regions are intact, 1 regions are incomplete, and 0 regions are questionable.

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
112.1Kbincomplete40141-12126 info_outlinePHAGE_Escher_RCS47_NC_042128(3)48.74%Show info_outline
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)
Region: The number assigned to the region.
Region Length: The length of the sequence of that region (in bp).
Completeness: A prediction of whether the region contains a intact or incomplete prophage based on the above criteria.
Score: The score of the region based on the above criteria.
# Total Proteins: The number of ORFs present in the region.
Region Position: The start and end positions of the region on the bacterial chromosome.
Most Common Phage: The phage(s) with the highest number of proteins most similar to those in the region.
GC %: The percentage of GC nucleotides of the region.

Criteria for scoring prophage regions (as intact, questionable, or incomplete):
Method 1:

  1. If the number of certain phage organism in this table is more than or equal to 100% of the total number of CDS of the region, the region is marked with total score 150. If less than 100%, method 2 and 3 will be used.
Method 2:
  1. If the number of certain phage organism in this table is more than 50% of the total number of CDS of the region, that phage organism is considered as the major potential phage for that region; the percentage of the total number of that phage organism in this table in the total number of proteins of the region is calculated and then multipled by 100; the percentage of the length of that phage organism in this table in the length of the region is calculated and then multipled by 50 (phage head's encapsulation capability is considered).
Method 3:
  1. If any of the specific phage-related keywords (such as 'capsid', 'head', 'integrase', 'plate', 'tail', 'fiber', 'coat', 'transposase', 'portal', 'terminase', 'protease' or 'lysin') are present, the score will be increased by 10 for each keyword found.
  2. If the size of the region is greater than 30 Kb, the score will be increased by 10.
  3. If there are at least 40 proteins in the region, the score will be increased by 10.
  4. If all of the phage-related proteins and hypothetical proteins constitute more than 70% of the total number of proteins in the region, the score will be increased by 10.
Compared the total score of method 2 with the total score of method 3, the bigger one is chosen as the total score of the region.
If the region's total score is less than 70, it is marked as incomplete; if between 70 to 90, it is marked as questionable; if greater than 90, it is marked as intact.

gi|00000000|ref|NZ_LXOM01000216.1| Salmonella enterica strain CU013109 PROKKA_contig000218, whole 12226, gc%: 48.74%

Download details as .txt file: detail.txt file_download

Hits against Virus and Prophage Database
Hits against Bacterial Database or GenBank File

Region 1, total 14 CDS

#CDS PositionBLAST HitE-ValueSequence
11..75PHAGE_Escher_RCS47_NC_042128: hypothetical protein; A7K97_RS28195; phage(gi100027)3.99e-10Showinfo_outline
2149..709PHAGE_Ralsto_Rs551_NC_047765: hypothetical protein; A7K97_RS19380; phage(gi100013)3.52e-42Showinfo_outline
3693..2357PHAGE_Pseudo_JBD18_NC_027986: hypothetical protein; A7K97_RS19385; phage(gi100013)1.89e-09Showinfo_outline
42290..3315PHAGE_Burkho_BcepMu_NC_005882: gp08; A7K97_RS19390; phage(gi48696918)4.50e-05Showinfo_outline
5complement(3504..4541)PROPHAGE_Escher_EDL933: putative transposase; A7K97_RS19395; phage(gi15803522)6.41e-120Showinfo_outline
65148..6041virulence genes transcriptional activator SpvR; A7K97_RS194000.0Showinfo_outline
76215..6379PHAGE_Edward_GF_2_NC_026611: putative lysozyme; A7K97_RS19405; phage(gi764162325)1.58e-17Showinfo_outline
86553..7320virulence protein SpvA; A7K97_RS194100.0Showinfo_outline
97283..7450hypothetical protein; A7K97_RS283950.0Showinfo_outline
107502..9283PHAGE_Pseudo_PaMx28_NC_028931: morphogenesis protein; A7K97_RS19415; phage(gi971757078)6.85e-06Showinfo_outline
119564..10289type III secretion system effector phosphothreonine lyase SpvC; A7K97_RS194200.0Showinfo_outline
1210550..11200SPI-2 type III secretion system effector cysteine hydrolase SpvD; A7K97_RS194250.0Showinfo_outline
13complement(11327..11752)PROPHAGE_Escher_Sakai: putative transposase; A7K97_RS19430; phage(gi15834436)8.83e-37Showinfo_outline
1411809..12126PHAGE_Clostr_c_st_NC_007581: putative IS transposase (OrfB); A7K97_RS19435; phage(gi80159731)6.38e-10Showinfo_outline
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

Viewer Options
Length: 12226 bps
Phages: 1
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Click on a region in the genome above to show details here.
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Click on a sequence to see details.
Lysis
Terminase
Portal Protein
Protease
Coat Protein
Tail Shaft
Attachment Site
Integrase
Phage-like Protein
Hypotheical Protein
Other
Transposase
Fiber Protein
Plate Protein
tRNA

Download data as .txt file: png_input file_download